Long Read Sequencing Report
Created on 2024-06-30 with Bamboo v0.1.0
FastQ Analysis Report
Input FASTQ Path: /data4/chs/00.software/Bamboo-main/test/data/ecoli_hifi.reads.fastq.gz
Output Path: /data4/chs/00.software/test_bamboo_fastqtobam4/sequence
Reference-Free QC
1. FastQ QC Summary
| Metric |
Value |
| Total_reads |
250 |
| Total_bases |
3709410 |
| Average_gc_content |
50.92 |
| Average_read_quality |
-1.90 |
| Read N50 |
14783 |
| Average_read_length |
14837.64 |
| <1kb read proportion |
0.00 |
| <2kb read proportion |
0.00 |
| <5kb read proportion |
0.00 |
| <10kb read proportion |
0.00 |
| <50kb read proportion |
1.00 |
2. Sequence Length
3. Sequencing Quality
3.1 Per-read quality distribution
3.2 Base quality along read relative position
3.3 Base quality in 5'/3' end
4. Length vs Quality
5. Read Content Metrics
5.1 Read GC%
5.2 Base content in 5'/3' end
5.3 Homo Distribution in 3' end
5.4 Heteropolymer Distribution in 3' end
5.5 Homo/Heteropolymer occurrences
Reference-based QC
Input BAM Path: /data4/chs/00.software/test_bamboo_fastqtobam4/alignment/sample.temp.bam
Reference Genome Path: /data4/chs/00.software/Bamboo-main/test/data/ecoli.reference.fasta.gz
Output Path: /data4/chs/00.software/test_bamboo_fastqtobam4/alignment
Reference-based QC
1. Bam QC Summary
| Total_reads | 311 |
|---|
| Unmapped_reads | 0 |
|---|
| Secondary_alignment_reads | 0 |
|---|
| Supplementary_alignment_reads | 61 |
|---|
| Forward_strand_reads | 148 |
|---|
| Reverse_strand_reads | 163 |
|---|
| Mismatch_count | 29258 |
|---|
| Mismatch_error_rate(percent) | 0.83 |
|---|
| Deletion_count | 86659 |
|---|
| Deletion_error_rate(percent) | 2.47 |
|---|
| Insertion_count | 36444 |
|---|
| Insertion_error_rate(percent) | 1.04 |
|---|
| Overall_error_count | 152361 |
|---|
| Overall_error_error_rate(percent) | 4.34 |
|---|
2. Coverage and bias
2.1 Coverage along chromosomes
2.2 Coverage fraction
2.3 GC% vs. Cov-normalized
3. Sequencing accuracy/error levels
3.1 Read acc% distribution
3.2 Error Rate Distribution
3.3 Relationship between read quality and error rate
4. Low complexity regions
4.1 Homo length vs. expansion/contraction rate
4.2 Heteropolymer length vs. expansion/contraction rate